Structural Fluctuations of a Cryptophane Host: A Molecular Dynamics Simulation

Cryptophanes are aromatic hosts which bind a variety of guests. Here, we describe a 20 ns molecular dynamics simulation of a particular cryptophane in water. This cryptophane features three pores which open onto a cavity where the guests bind. The molecular dynamics simulation in combination with a surfacing algorithm provides information on the frequency with which these pores open wide enough to admit guest molecules of any given size. We discuss these fluctuations and their possible consequences for binding kinetics.